data_S38
#
_chem_comp.id S38
_chem_comp.name 4-cyano-N-[(1S,2R)-2-phenylcyclopropyl]benzamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H14 N2 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-09-27
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 262.306
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code S38
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 3ANS
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
S38 C1 C1 C 0 1 Y N N N N N 54.636 54.092 73.042 -4.020 1.096 -0.508 C1 S38 1
S38 C2 C2 C 0 1 Y N N N N N 53.688 53.187 73.452 -4.943 0.299 0.174 C2 S38 2
S38 C3 C3 C 0 1 Y N N N N N 53.108 53.252 74.698 -4.521 -0.873 0.805 C3 S38 3
S38 C4 C4 C 0 1 Y N N N N N 53.489 54.250 75.559 -3.196 -1.244 0.755 C4 S38 4
S38 C5 C5 C 0 1 Y N N N N N 54.434 55.158 75.148 -2.273 -0.448 0.073 C5 S38 5
S38 C6 C6 C 0 1 Y N N N N N 55.017 55.098 73.902 -2.694 0.725 -0.558 C6 S38 6
S38 C7 C7 C 0 1 N N N N N N 54.862 56.220 76.043 -0.850 -0.846 0.020 C7 S38 7
S38 N8 N8 N 0 1 N N N N N N 53.919 56.813 76.833 0.041 -0.077 -0.638 N8 S38 8
S38 C9 C9 C 0 1 N N S N N N 54.288 58.046 77.439 1.451 -0.472 -0.691 C9 S38 9
S38 C10 C10 C 0 1 N N R N N N 54.660 58.104 78.885 2.486 0.634 -0.902 C10 S38 10
S38 C11 C11 C 0 1 N N N N N N 53.452 58.834 78.399 2.170 -0.344 -2.035 C11 S38 11
S38 C12 C12 C 0 1 Y N N N N N 55.850 58.843 79.336 3.814 0.487 -0.206 C12 S38 12
S38 C13 C13 C 0 1 Y N N N N N 56.839 59.240 78.462 4.231 1.446 0.699 C13 S38 13
S38 C14 C14 C 0 1 Y N N N N N 57.953 59.921 78.901 5.449 1.310 1.338 C14 S38 14
S38 C15 C15 C 0 1 Y N N N N N 58.096 60.216 80.237 6.251 0.216 1.073 C15 S38 15
S38 C16 C16 C 0 1 Y N N N N N 57.119 59.822 81.123 5.834 -0.744 0.169 C16 S38 16
S38 C17 C17 C 0 1 Y N N N N N 56.009 59.145 80.670 4.614 -0.610 -0.467 C17 S38 17
S38 O18 O18 O 0 1 N N N N N N 56.043 56.513 76.044 -0.483 -1.866 0.569 O18 S38 18
S38 C19 C19 C 0 1 N N N N N N 53.297 52.149 72.579 -6.321 0.685 0.226 C19 S38 19
S38 N20 N20 N 0 1 N N N N N N 53.006 51.281 71.869 -7.414 0.991 0.267 N20 S38 20
S38 H1 H1 H 0 1 N N N N N N 55.077 54.016 72.059 -4.346 2.000 -1.000 H1 S38 21
S38 H3 H3 H 0 1 N N N N N N 52.363 52.528 74.994 -5.235 -1.489 1.332 H3 S38 22
S38 H4 H4 H 0 1 N N N N N N 53.053 54.320 76.544 -2.870 -2.150 1.243 H4 S38 23
S38 H6 H6 H 0 1 N N N N N N 55.758 55.825 73.605 -1.981 1.340 -1.085 H6 S38 24
S38 HN8 HN8 H 0 1 N N N N N N 53.018 56.403 76.978 -0.252 0.737 -1.076 HN8 S38 25
S38 H9 H9 H 0 1 N N N N N N 54.753 58.292 76.473 1.730 -1.306 -0.047 H9 S38 26
S38 H10 H10 H 0 1 N N N N N N 54.857 57.352 79.664 2.118 1.656 -1.002 H10 S38 27
S38 H11 H11 H 0 1 N N N N N N 53.199 59.904 78.423 2.922 -1.095 -2.276 H11 S38 28
S38 H11A H11A H 0 0 N N N N N N 52.392 58.739 78.678 1.594 0.033 -2.880 H11A S38 29
S38 H13 H13 H 0 1 N N N N N N 56.738 59.012 77.411 3.605 2.301 0.906 H13 S38 30
S38 H14 H14 H 0 1 N N N N N N 58.714 60.223 78.197 5.775 2.060 2.044 H14 S38 31
S38 H15 H15 H 0 1 N N N N N N 58.966 60.751 80.587 7.203 0.110 1.571 H15 S38 32
S38 H16 H16 H 0 1 N N N N N N 57.223 60.044 82.175 6.460 -1.599 -0.038 H16 S38 33
S38 H17 H17 H 0 1 N N N N N N 55.248 58.845 81.375 4.286 -1.362 -1.170 H17 S38 34
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
S38 C1 C2 DOUB Y N 1
S38 C1 C6 SING Y N 2
S38 C2 C3 SING Y N 3
S38 C2 C19 SING N N 4
S38 C3 C4 DOUB Y N 5
S38 C4 C5 SING Y N 6
S38 C5 C6 DOUB Y N 7
S38 C5 C7 SING N N 8
S38 C7 N8 SING N N 9
S38 C7 O18 DOUB N N 10
S38 N8 C9 SING N N 11
S38 C9 C10 SING N N 12
S38 C9 C11 SING N N 13
S38 C10 C11 SING N N 14
S38 C10 C12 SING N N 15
S38 C12 C13 DOUB Y N 16
S38 C12 C17 SING Y N 17
S38 C13 C14 SING Y N 18
S38 C14 C15 DOUB Y N 19
S38 C15 C16 SING Y N 20
S38 C16 C17 DOUB Y N 21
S38 C19 N20 TRIP N N 22
S38 C1 H1 SING N N 23
S38 C3 H3 SING N N 24
S38 C4 H4 SING N N 25
S38 C6 H6 SING N N 26
S38 N8 HN8 SING N N 27
S38 C9 H9 SING N N 28
S38 C10 H10 SING N N 29
S38 C11 H11 SING N N 30
S38 C11 H11A SING N N 31
S38 C13 H13 SING N N 32
S38 C14 H14 SING N N 33
S38 C15 H15 SING N N 34
S38 C16 H16 SING N N 35
S38 C17 H17 SING N N 36
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
S38 SMILES ACDLabs 12.01 "O=C(NC2CC2c1ccccc1)c3ccc(C#N)cc3"
S38 SMILES_CANONICAL CACTVS 3.370 "O=C(N[C@H]1C[C@@H]1c2ccccc2)c3ccc(cc3)C#N"
S38 SMILES CACTVS 3.370 "O=C(N[CH]1C[CH]1c2ccccc2)c3ccc(cc3)C#N"
S38 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1ccc(cc1)[C@H]2C[C@@H]2NC(=O)c3ccc(cc3)C#N"
S38 SMILES "OpenEye OEToolkits" 1.7.0 "c1ccc(cc1)C2CC2NC(=O)c3ccc(cc3)C#N"
S38 InChI InChI 1.03 InChI=1S/C17H14N2O/c18-11-12-6-8-14(9-7-12)17(20)19-16-10-15(16)13-4-2-1-3-5-13/h1-9,15-16H,10H2,(H,19,20)/t15-,16+/m1/s1
S38 InChIKey InChI 1.03 RPFFDFASGIBGIP-CVEARBPZSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
S38 "SYSTEMATIC NAME" ACDLabs 12.01 4-cyano-N-[(1S,2R)-2-phenylcyclopropyl]benzamide
S38 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 4-cyano-N-[(1S,2R)-2-phenylcyclopropyl]benzamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
S38 'Create component' 2010-09-27 PDBJ
S38 'Modify aromatic_flag' 2011-06-04 RCSB
S38 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
S38 C1 C 7.647 -3.275 1
S38 C2 C 6.348 -4.024 2
S38 C3 C 5.049 -3.275 3
S38 C4 C 5.049 -1.774 4
S38 C5 C 6.348 -1.024 5
S38 C6 C 7.647 -1.774 6
S38 C7 C 6.348 0.475 7
S38 N8 N 7.647 1.226 8
S38 C9 C 7.647 2.725 9
S38 C10 C 6.897 4.024 10
S38 C11 C 8.397 4.024 11
S38 C12 C 5.598 4.774 12
S38 C13 C 5.598 6.274 13
S38 C14 C 4.299 7.024 14
S38 C15 C 3.000 6.274 15
S38 C16 C 3.000 4.774 16
S38 C17 C 4.299 4.024 17
S38 O18 O 5.049 1.226 18
S38 C19 C 6.348 -5.524 19
S38 N20 N 6.348 -7.024 20
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
S38 C1 C2 DOUBLE NONE 1
S38 C1 C6 SINGLE NONE 2
S38 C2 C3 SINGLE NONE 3
S38 C2 C19 SINGLE NONE 4
S38 C3 C4 DOUBLE NONE 5
S38 C4 C5 SINGLE NONE 6
S38 C5 C6 DOUBLE NONE 7
S38 C5 C7 SINGLE NONE 8
S38 C7 N8 SINGLE NONE 9
S38 C7 O18 DOUBLE NONE 10
S38 C9 N8 SINGLE BEGINDASH 11
S38 C9 C10 SINGLE NONE 12
S38 C9 C11 SINGLE NONE 13
S38 C10 C11 SINGLE NONE 14
S38 C10 C12 SINGLE BEGINWEDGE 15
S38 C12 C13 DOUBLE NONE 16
S38 C12 C17 SINGLE NONE 17
S38 C13 C14 SINGLE NONE 18
S38 C14 C15 DOUBLE NONE 19
S38 C15 C16 SINGLE NONE 20
S38 C16 C17 DOUBLE NONE 21
S38 C19 N20 TRIPLE NONE 22
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
S38 MurckoScaffold S1 scaffold 'O=C(N[C@H]1C[C@@H]1c1ccccc1)c1ccccc1' InChI=1S/C16H15NO/c18-16(13-9-5-2-6-10-13)17-15-11-14(15)12-7-3-1-4-8-12/h1-10,14-15H,11H2,(H,17,18)/t14-,15+/m1/s1 PNDHLCFURACDRW-CABCVRRESA-N
S38 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
S38 cyclopropane F2 fragment C1CC1 InChI=1S/C3H6/c1-2-3-1/h1-3H2 LVZWSLJZHVFIQJ-UHFFFAOYSA-N
S38 phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
S38 C1 S1 1
S38 C2 S1 1
S38 C3 S1 1
S38 C4 S1 1
S38 C5 S1 1
S38 C6 S1 1
S38 C7 S1 1
S38 N8 S1 1
S38 C9 S1 1
S38 C10 S1 1
S38 C11 S1 1
S38 C12 S1 1
S38 C13 S1 1
S38 C14 S1 1
S38 C15 S1 1
S38 C16 S1 1
S38 C17 S1 1
S38 O18 S1 1
S38 N8 F1 1
S38 C7 F1 1
S38 O18 F1 1
S38 C5 F1 1
S38 C9 F2 1
S38 C10 F2 1
S38 C11 F2 1
S38 C1 F3 1
S38 C2 F3 1
S38 C3 F3 1
S38 C4 F3 1
S38 C5 F3 1
S38 C6 F3 1
S38 C12 F3 2
S38 C13 F3 2
S38 C14 F3 2
S38 C15 F3 2
S38 C16 F3 2
S38 C17 F3 2
#
_pdbe_chem_comp_rdkit_properties.comp_id S38
_pdbe_chem_comp_rdkit_properties.exactmw 262.111
_pdbe_chem_comp_rdkit_properties.amw 262.312
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.176
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 137.139
_pdbe_chem_comp_rdkit_properties.tpsa 52.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.680
_pdbe_chem_comp_rdkit_properties.CrippenMR 75.413
_pdbe_chem_comp_rdkit_properties.chi0v 9.803
_pdbe_chem_comp_rdkit_properties.chi1v 5.375
_pdbe_chem_comp_rdkit_properties.chi2v 2.332
_pdbe_chem_comp_rdkit_properties.chi3v 2.332
_pdbe_chem_comp_rdkit_properties.chi4v 1.360
_pdbe_chem_comp_rdkit_properties.chi0n 23.803
_pdbe_chem_comp_rdkit_properties.chi1n 12.322
_pdbe_chem_comp_rdkit_properties.chi2n 2.332
_pdbe_chem_comp_rdkit_properties.chi3n 2.332
_pdbe_chem_comp_rdkit_properties.chi4n 1.360
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.600
_pdbe_chem_comp_rdkit_properties.kappa1 4.195
_pdbe_chem_comp_rdkit_properties.kappa2 5.181
_pdbe_chem_comp_rdkit_properties.kappa3 2.548
_pdbe_chem_comp_rdkit_properties.Phi 1.087
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
S38 UniChem 'PubChem TPHARMA' 118044363
S38 UniChem BindingDb 50336821
S38 UniChem PubChem 49837852
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
S38 C1 4.439 0.329 2.403 ETKDGv3 1
S38 C2 5.295 0.123 1.392 ETKDGv3 2
S38 C3 4.787 0.036 0.006 ETKDGv3 3
S38 C4 3.478 0.173 -0.241 ETKDGv3 4
S38 C5 2.522 0.419 0.871 ETKDGv3 5
S38 C6 2.994 0.479 2.132 ETKDGv3 6
S38 C7 1.071 0.571 0.603 ETKDGv3 7
S38 N8 0.599 0.971 -0.692 ETKDGv3 8
S38 C9 -0.827 1.012 -0.997 ETKDGv3 9
S38 C10 -1.426 -0.369 -1.238 ETKDGv3 10
S38 C11 -1.159 0.562 -2.417 ETKDGv3 11
S38 C12 -2.877 -0.561 -0.841 ETKDGv3 12
S38 C13 -3.266 -1.777 -0.415 ETKDGv3 13
S38 C14 -4.665 -2.025 -0.011 ETKDGv3 14
S38 C15 -5.564 -1.037 -0.063 ETKDGv3 15
S38 C16 -5.159 0.303 -0.526 ETKDGv3 16
S38 C17 -3.892 0.534 -0.894 ETKDGv3 17
S38 O18 0.239 0.352 1.526 ETKDGv3 18
S38 C19 6.704 -0.022 1.648 ETKDGv3 19
S38 N20 7.836 -0.139 1.854 ETKDGv3 20
S38 H1 4.794 0.392 3.425 ETKDGv3 21
S38 H3 5.472 -0.149 -0.812 ETKDGv3 22
S38 H4 3.128 0.076 -1.260 ETKDGv3 23
S38 H6 2.328 0.652 2.969 ETKDGv3 24
S38 HN8 1.263 1.382 -1.385 ETKDGv3 25
S38 H9 -1.446 1.807 -0.532 ETKDGv3 26
S38 H10 -0.718 -1.224 -1.161 ETKDGv3 27
S38 H11 -2.042 1.062 -2.865 ETKDGv3 28
S38 H11A -0.284 0.267 -3.035 ETKDGv3 29
S38 H13 -2.559 -2.597 -0.361 ETKDGv3 30
S38 H14 -4.960 -3.010 0.329 ETKDGv3 31
S38 H15 -6.589 -1.218 0.234 ETKDGv3 32
S38 H16 -5.890 1.100 -0.567 ETKDGv3 33
S38 H17 -3.627 1.527 -1.230 ETKDGv3 34
#